Lots of man hours invested in prepping the woodwork for priming and again before the finish coats are sprayed. The bondo is applied due to its tendency to perfectly same and not shrink. This level of preparation is beyond the standard I’ve seen in other projects. Renovations especially tend to have horrible paint quality. If you see a renovation with orange peel type finish or even a brushed Finish then you can be sure the paint was done quickly and cheaply. A lot of filling and sanding is needed to achieve an excellent finish
The patches are either nail holes or dings in the woodwork. It will disappear under the next coat of lacquer.